The present invention relates to a method to produce a biochip and to a biochip, said biochip being composed particularly of biological probes grafted onto a conductive polymer.
Biological analysis devices, for example DNA chips, represent high-performance tools for the parallel analysis of a large number of genes or DNA or RNA sequences. Their operating principle is based on the hybridisation or pairing property of two strands of complementary sequences in order to reconstitute the DNA double helix. To do this, oligonucleotide probes of a known sequence, immobilised on a support substrate, are placed in the presence of targets extracted from a biological specimen under analysis, and labelled using fluorescent markers.
The hybridisation is then identified and the sequence detected by analysing the surface of the chip with a suitable marker for example to detect the sequence by fluorescence.
Very different technologies have been used to produce these probe matrices. Various immobilisation or grafting techniques of probes onto different substrates have been the subject of significant studies and industrial developments.
1. State of the Related Art
There are essentially three chemical probe addressing methods which represent different approaches to the production and use of probes for different fields of application. They consist of photochemical addressing, mechanical addressing, for example by micropipetting using a dispersion robot, and electrochemical addressing.
For example, electrochemical addressing may be used for oligonucleotide probes. To do this, individually addressed electrode matrices are produced on a glass substrate.
The biological probe immobilisation principle is based on the electropolymerisation deposition of a copolymer of pyrrole and pyrrole substituted by an oligonucleotide (Py-ODN), comprising an oligonucleotide grafted onto a pyrrole nucleus either directly, or indirectly by means of a spacer.
In order to develop massively parallel biological analysis systems, with a high capacity or active site density, it is necessary to be able to address a large number of probes.
Methods using electrochemical addressing require both a large electrode and connection matrix and a multiplexer to index each of the chip""s sites electrically. In addition, in these methods, it is necessary to carry out electropolymerisation by immersing the entire chip successively in solutions of each of the Py-ODNs contained in the cell. Therefore, these methods are limited to low-density chips, i.e. comprising approximately one hundred probes, for limited and specific applications.
Other methods have been described in the prior art, advantageously replacing individual electrical addressing by mechanical addressing. However, a disadvantage remains, that of carrying out electropolymerisations in microtroughs, with a solution volume of the order of one nanolitre, for which it is necessary to delay evaporation after micropipetting of all the probes on the insert so that electropolymerisation may take place.
2. Description of the Invention
The aim of the present invention is specifically to solve the above-mentioned problems by providing a method to produce a biochip composed particularly of biological probes grafted onto a conductive polymer, said method particularly offering the advantage of only requiring the use of a single solution of a mixture of suitable proportions of pyrrole and substituted pyrrole (Py and Py-R-F or F and a reactive chemical function and R is an aliphatic or aromatic spacer group) for a single collective electrodeposition on all the microtroughs.
The method according to the invention is characterised in that it comprises the following steps:
a) structuring of a substrate so as to obtain on said substrate microtroughs comprising in their base a layer of a material capable of initiating and promoting the adhesion onto said layer of a film of a pyrrole and functionalised pyrrole copolymer by electropolymerisation,
b) collective electropolymerisation, so as to form an electropolymerised film of a pyrrole and functionalised pyrrole copolymer on the base of said microtroughs, on the layer of said material, using a pyrrole and functionalised pyrrole solution, in the presence of suitable chemical reagents for said electropolymerisation,
c) direct or indirect fixation of a biological probe onto the functionalised pyrrole, by injecting a biological probe solution, either in one or more microtroughs in the presence of chemical reagents required for the direct or indirect fixation of this biological probe onto the functionalised pyrrole.
According to the invention, the layer of material capable of initiating and promoting the adhesion of a film of a pyrrole and functionalised pyrrole copolymer by electropolymerisation onto said layer may be a metallic layer, step a) mentioned above possibly comprising a deposition step of said metallic layer onto the substrate, and a deposition step of a layer of resin or polymer onto the metallic layer and development or engraving of said layer so as to form microtroughs, wherein the base is composed at least partly of the metallic layer.
According to the invention, the metallic layer may be, for example, a layer of gold, a layer of copper or silver or aluminium.
According to the invention, the substrate may be for example a silicon insert, a glass insert or a flexible plastic support if required.
According to another embodiment of the present invention, the step a) may also comprise a treatment step of the gold layer at the base of the microtroughs in the presence of a functionalised pyrrole for example with a thiol group so as to form a monolayer of pyrrole onto said metallic layer, for example on said gold layer, at the base of said microtroughs. This monolayer is capable of initiating and promoting the adhesion of a polypyrrole film by electropolymerisation as demonstrated by R. Simon et al., J. Am. Chem. Soc., 1982, 104, 2031). This is a self-assembled monolayer SAM of a functionalised pyrrole for its adhesion onto the base of the microtroughs.
According to the invention, the functionalised pyrrole may be a pyrrole which comprises a chemical group enabling its fixation by covalent bonding with the metallic layer, and/or with the biological probe. In the case of its fixation to the metallic layer, for example to the gold layer, a functionalised pyrrole with a thiol or disulphide group may also be used.
For example, the functionalised pyrrole with a thiol group may have the following chemical formula: 
wherein n may have a value ranging from 1 to 10, for example n may be equal to 6.
For a metallic aluminium probe, a functionalised pyrrole with a xe2x80x94COOH group may be chosen.
According to another embodiment of the present invention, the substrate may be a silicon insert and the layer capable of initiating and promoting the adhesion onto said layer of a polypyrrole film by electropolymerisation may be a layer of silane comprising an alignment of pyrrole sites. Step a) of the method according to the present invention may in this case comprise a deposition step of a layer of resin on the silicon insert, said silicon insert being coated with an SiO2 film, and engraving of said resin layer so as to form the microtroughs wherein the base is composed at least partly of the SiO2 film; and a microtrough treatment step by means of a functionalised silanisation agent with a pyrrole so as to fix, on the SiO2 film, in the base of the microtroughs, the silane layer comprising an alignment of pyrrole sites.
According to the invention, the silanisation agent may be chosen in a group comprising N-(3-(trimethoxy silyl) propyl) pyrrole, or any other functionalised pyrrole with an xe2x80x94SiCl3 or xe2x80x94Si(OMe)3 group. The SiO2 film may be a natural SiO2 film present on silicon inserts.
According to the invention, irrespective of the embodiment, the resin may be a photosensitive resin, wherein masking, insolation and development are used to form the microtroughs.
According to the invention, the collective electropolymerisation in step b) of the method may be carried out for example by immersing the structured substrate obtained in step a) mentioned above in an electrolytic bath comprising a solution of pyrrole, functionalised pyrrole, and suitable chemical reagents for electropolymerisation, in the presence of a counter-electrode to the working electrode which is immersed in the electrolytic bath and is independent of the structured substrate.
According to the invention, in this step b), the functionalised pyrrole may be a pyrrole comprising a group chosen in a set comprising an NH2 group, a thiol group a succinimide ester group, a trimethoxy silyl group, a carboxyl, aldehyde and isothiocyanate group.
According to the invention, the functionalised pyrrole by electropolymerisation may for example be chosen from one of the following compounds: 
PYRROLE 
N-ETHYLAMINE PYRROLE 
N(3-(TRIMETHOXY SILYL) PROPYL) PYRROLE 
Functionalised PYRROLE with a thiol 
Functionalised PYRROLE in 3xe2x80x2 by a succinimydyl ester.
According to the invention, the electrolytic bath may be a mixture of pyrrole and functionalised pyrrole in suitable proportions to form a film comprising a required number of units of functionalised pyrrole. In this way, the method according to the invention makes it possible to choose the number of biological probes per microtrough, since according to this method, the biological probes are fixed, either directly or indirectly on said functionalised pyrroles.
The next step c) of the method according to the invention consists of a direct or indirect fixation of a biological probe onto the functionalised pyrrole.
According to the invention, when the fixation of the biological probe is indirect, the step c) of the method according to the invention may also comprise, before the fixation of the biological probe, a collective fixation of a cross-linking agent on the functionalised pyrrole, in the presence of suitable chemical reagents, said cross-linking agent comprising a first function enabling its fixation onto the functionalised pyrrole, and a second function enabling the fixation of the biological probe on said cross-linking agent.
According to the invention, the cross-linking agent may for example be a bi-functional cross-linking agent.
The cross-linking agent may for example comprise an N-hydroxysuccinimide ester function and a maleimide function.
According to the invention, the cross-linking agent may for example be chosen from one of the following compounds; 
N-hydroxysuccinimide ester maleic function
SMPB
succinimidyl 4-(p-maleimidophenyl)butyrate 
GMBS
N-maleimidobutyryloxy succinimide ester,
a dialdehyde of the type 
GLUTARALDEHYDE,
a diisothiocyanate of the type 
1,4-PHENYLENE DIISOTHIOCYANATE, 
SUCCINIC ANHYDRIDE OR SUCCINIC ACID
or a derivative of these compounds.
All the bi-functional cross-linking agents mentioned above are suitable for functionalised polypyrroles with the xe2x80x94CH2xe2x80x94CH2xe2x80x94NH2 group in position 1 on nitrogen. However, electropolymerisation with a functionalised pyrrole with other groups is also possible. For example, Py-CH2xe2x80x94CH2xe2x80x94NH2, Py-SH, Py-succinimidyl ester (in 3), Py-hydrazine with a substitution in 1 on nitrogen or in 3 on the pyrrole cycle, making it possible to immobilise the oligonucleotides, either directly or by means of a cross-linking agent, for example a bi-functional agent.
The following cross-linking agents may therefore be used in the method according the present invention:
a) a glutaraldehyde type dialdehyde, which may react on the NH2 function of the polypyrrole film (collective step) and then on the NH2 function of an oligonucleotide terminated for example by a phosphate comprising an amino group, by an individual step in the microtroughs;
b) a diisothiocyanate which may also react on the amine function of the functionalised polypyrrole at one end (collective step) and then on an amine function of an oligonucleotide terminated by a phosphate with a functionalised spacer group with NH2;
c) a succinic anhydride, which for each opening, comprises two acid functions capable of reacting on the NH2 groups of the polypyrrole and on the NH2 groups of a functionalised oligonucleotide with NH2.
According to the invention, the biological probe which will be the source of the specificity of the manufactured biochip, may be chosen for example from an oligonucleotide, a DNA, an RNA, a peptide, a glucide, a lipid, a protein, an antibody, an antigen.
According to the invention, the biological probe is preferentially functionalised to be able to be fixed either directly or indirectly on the functionalised pyrrole. The purpose of this functionalisation is to fix on the biological probe a chemical group capable of forming a covalent bond between the biological probe and the functionalised pyrrole.
It may be for example functionalised with a thiol group, with an NH2 group, aldehyde, a xe2x80x94COOH group or an acid phosphate group.
For example, when the biological probe is an oligonucleotide, it may be functionalised with a thiol group SH. The functionalised oligonucleotides with Sxe2x80x94H may be prepared according to a known procedure, for example at the end of an automated oligonucleotide synthesis.
If it is easier to use functionalised oligonucleotides with NH2, it is possible for example to synthesise a functionalised pyrrole with an Sxe2x80x94H for copolymerisation, to use for example SMPB with its two specific functions and immobilise the functionalised oligonucleotides with NH2 by covalent bonding with the succinamide function of this cross-linking agent.
In the case of oligonucleotides terminated in 3xe2x80x2 by an N-methyl uridine nucleotide, an oxidation reaction on this function makes it possible to obtain a functionalised oligonucleotide with an aldehyde function, capable of reacting directly, i.e. for example without the bi-functional agent on the functionalised polypyrrole with NH2.
To functionalise an oligonucleotide with an NH2 function, one of the methods that may be used according to the method of the present invention may consist of coupling the oligonucleotide and commercially available N-trifluoroacetyl-6 amino hexyl-2 cyanoethyl NNxe2x80x2-diisopropyl phosphoramidite.
In addition, a functionalised oligonucleotide with NH2 may for example be converted into an oligonucleotide terminated by a thiol with a reaction with dithiobis(succinimidylpropionate).
The functionalised probe oligonucleotides may for example be taken up by micropipetting in microwells and injected into the microtroughs for example by means of a dispensing microrobot or by jet printing. These devices are well-known to those skilled in the art.
The method according to the present invention makes it possible advantageously to choose the number of probes per active site, i.e. per microtrough by adjusting the proportion of functionalised pyrrole with reference to the pyrrole.
The required probe density may be monitored for example by fixing oligonucleotides labelled at the chain ends by a biotin and using streptavidine-Cy3 detection by a surface analysis of the chip using conventional fluorescence detection methods.
Another advantage of the method according to the invention lies in the fact that both collective operations, electropolymerisation and fixation of the cross-linking agent if applicable, may be carried out in batches on a large number of inserts in parallel.
The inserts having undergone step a) and b) of the method according to the invention are also referred to as xe2x80x9cblank biochipsxe2x80x9d. They are ready to undergo the direct or indirect fixation step of a biological probe, for example of an oligonucleotide according to the present invention.
In this way, the method according to the invention makes it possible for example to produce an oligonucleotide chip comprising in this order:
a silicon substrate coated in silica, and a functionalised silane layer with pyrrole, or
a gold layer or a silane layer comprising pyrrole sites, or
a gold layer with or without an electropolymerisation promotion and adherence layer (based on a functionalised pyrrole with an xe2x80x94SH thiol), or
an aluminium layer with a functionalised pyrrole with a xe2x80x94COOH,
and a resin layer wherein microtroughs have been produced such that the base of said microtroughs is composed at least partly of the gold layer or the silane layer comprising pyrrole sites,
and a layer of pyrrole and functionalised pyrrole copolymer, fixed on the gold layer or the silane layer comprising pyrrole sites forming the base of said microtroughs, the functionalised pyrrole being bound to a bi-functional cross-linking agent or not,
and an oligonucleotide fixed directly on the functionalised pyrrole, or indirectly on the functionalised pyrrole by means of the cross-linking agent bound with the pyrrole.
The present invention""s other advantages and characteristics will be seen more clearly upon reading the following description, which is naturally given as an illustration and is not restrictive, with reference to the appended figures.